Ugandan President Yoweri Museveni on Tuesday removed the country's powerful military intelligence chief, just weeks after he was sanctioned by the United States over human rights violations.

Major General Abel Kandiho, who has been the commander of the feared Chieftaincy of Military Intelligence since January 2017, has faced accusations of abuses including beatings, sexual assault and electrocution.

Kandiho will take up a new role as security envoy in South Sudan and has been replaced in the military intelligence role by former special forces commander Major General James Birungi, Uganda's defence ministry said in a statement.

"This is one of the routine transfers and reassignments and is in line with the prerogative of the commander-in-chief to transfer, reassign and appoint officers," ministry spokesman Ronald Kakurungu said.

The US Treasury last month slapped Kandiho with sanctions, citing his and his office's involvement in serious human rights violations.

People arrested by his bureau were "subjected to horrific beatings and other egregious acts by (military intelligence) officials, including sexual abuse and electrocutions, often resulting in significant long-term injury and even death," it said in a statement.

Kandiho was, the US statement said, sometimes personally involved in leading interrogations of detained individuals, often singled out for their political views, their nationality or for criticising the government.

The Ugandan military hit back, saying it was disappointed the sanctions were imposed "without due process and in total disregard of the principle of 'fair hearing'."

The East African country has long suffered a series of crackdowns aimed at stamping out dissent, with journalists attacked, lawyers jailed, election monitors prosecuted and opposition leaders violently muzzled.

Kandiho's removal comes days after Museveni's son Muhoozi Kainerugaba -- a general rumoured to be a possible successor to his 77-year-old father -- met Rwandan President Paul Kagame following years of tension between the two neighbours.

Rwandan officials have in recent years accused Kandiho of working with dissidents to kidnap Rwandan citizens in Uganda.

Kainerugaba on Tuesday congratulated Kandiho and his replacement on their new roles.

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